COL2A1 (collagen type II alpha 1 chain) - Rat Genome Database

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Pathways
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Gene: COL2A1 (collagen type II alpha 1 chain) Chlorocebus sabaeus
Analyze
Symbol: COL2A1
Name: collagen type II alpha 1 chain
RGD ID: 18414204
Description: ENCODES a protein that exhibits extracellular matrix structural constituent (inferred); extracellular matrix structural constituent conferring tensile strength (inferred); identical protein binding (inferred); INVOLVED IN anterior head development (ortholog); bone development (ortholog); cartilage condensation (ortholog); PARTICIPATES IN syndecan signaling pathway; ASSOCIATED WITH achondrogenesis type II (ortholog); Animal Disease Models (ortholog); arthritis (ortholog); FOUND IN collagen-containing extracellular matrix (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: collagen alpha-1(II) chain
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: ChlSab1.1 - Green Monkey 1.1 Assembly
Position:
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11144,196,213 - 44,227,718 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1144,196,094 - 44,227,468 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666037202,151,602 - 202,183,142 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
achondrogenesis type II  (ISO)
Animal Disease Models  (ISO)
arthritis  (ISO)
asphyxiating thoracic dystrophy  (ISO)
bone resorption disease  (ISO)
Bronchial Fistula  (ISO)
cartilage disease  (ISO)
cataract  (ISO)
chondrosarcoma  (ISO)
chorioretinitis  (ISO)
cleft palate  (ISO)
Collagenopathy, Type 2 Alpha 1  (ISO)
congenital heart disease  (ISO)
connective tissue disease  (ISO)
Craniofacial Abnormalities  (ISO)
Czech Dysplasia, Metatarsal Type  (ISO)
degenerative disc disease  (ISO)
developmental dysplasia of the hip  (ISO)
Dwarfism  (ISO)
Edema  (ISO)
Erythema  (ISO)
Experimental Arthritis  (ISO)
eye disease  (ISO)
Femur Head Necrosis  (ISO)
Fetal Growth Retardation  (ISO)
fundus dystrophy  (ISO)
genetic disease  (ISO)
Hearing Loss  (ISO)
hereditary breast ovarian cancer syndrome  (ISO)
High Myopia  (ISO)
Hyaloideoretinal Degeneration of Wagner  (ISO)
Hyperplasia  (ISO)
hypochondrogenesis  (ISO)
hypothyroidism  (ISO)
Inflammation  (ISO)
intellectual disability  (ISO)
Kniest dysplasia  (ISO)
Legg-Calve-Perthes disease  (ISO)
Maffucci syndrome  (ISO)
Marfan syndrome  (ISO)
MASS Syndrome  (ISO)
melanoma  (ISO)
multiple epiphyseal dysplasia with myopia and deafness  (ISO)
myopia  (ISO)
orofacial cleft 1  (ISO)
osteoarthritis  (ISO)
Osteoarthritis with Mild Chondrodysplasia  (ISO)
osteochondrodysplasia  (ISO)
otospondylomegaepiphyseal dysplasia, autosomal dominant  (ISO)
otospondylomegaepiphyseal dysplasia, autosomal recessive  (ISO)
Prognathism  (ISO)
retinal detachment  (ISO)
retinitis pigmentosa  (ISO)
Rhegmatogenous Retinal Detachment, Autosomal Dominant  (ISO)
rheumatoid arthritis  (ISO)
sensorineural hearing loss  (ISO)
spondyloarthropathy  (ISO)
spondyloepimetaphyseal dysplasia  (ISO)
spondyloepimetaphyseal dysplasia, Strudwick type  (ISO)
spondyloepiphyseal dysplasia congenita  (ISO)
spondyloepiphyseal dysplasia Stanescu type  (ISO)
spondylometaphyseal dysplasia  (ISO)
spondylometaphyseal dysplasia corner fracture type  (ISO)
spondyloperipheral dysplasia  (ISO)
Stargardt disease  (ISO)
Stickler syndrome  (ISO)
Stickler syndrome 1  (ISO)
Stickler Syndrome, Type I, Nonsyndromic Ocular  (ISO)
synovitis  (ISO)
Torrance type platyspondylic dysplasia  (ISO)
Vitreoretinopathy with Phalangeal Epiphyseal Dysplasia  (ISO)
Weight Loss  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
animal organ morphogenesis  (IEA)
anterior head development  (IEA,ISO)
bone development  (IEA,ISO)
cartilage condensation  (IEA,ISO)
cartilage development  (IEA,ISO)
cartilage development involved in endochondral bone morphogenesis  (IEA,ISO)
cellular response to BMP stimulus  (IEA,ISO)
cellular response to insulin-like growth factor stimulus  (ISO)
cellular response to mechanical stimulus  (ISO)
cellular response to nicotine  (ISO)
cellular response to parathyroid hormone stimulus  (ISO)
cellular response to peptide hormone stimulus  (ISO)
cellular response to retinoic acid  (ISO)
cellular response to tumor necrosis factor  (ISO)
cellular response to vitamin E  (ISO)
central nervous system development  (IEA)
chondrocyte differentiation  (IEA,ISO)
collagen fibril organization  (IEA,ISO)
embryonic skeletal joint morphogenesis  (IEA)
endochondral ossification  (IEA,ISO)
extrinsic apoptotic signaling pathway in absence of ligand  (IEA,ISO)
growth plate cartilage development  (ISO)
heart morphogenesis  (IEA,ISO)
inner ear development  (IEA,ISO)
inner ear morphogenesis  (IEA,ISO)
limb bud formation  (IEA)
limb morphogenesis  (IEA,ISO)
negative regulation of extrinsic apoptotic signaling pathway in absence of ligand  (IEA,ISO)
notochord development  (IEA)
ossification  (IEA)
otic vesicle development  (IEA)
proteoglycan metabolic process  (IEA,ISO)
regulation of gene expression  (IEA,ISO)
response to fibroblast growth factor  (ISO)
response to mechanical stimulus  (ISO)
response to X-ray  (ISO)
roof of mouth development  (IEA,ISO)
sensory perception of sound  (IEA)
skeletal system development  (IEA)
skeletal system morphogenesis  (IEA,ISO)
tissue homeostasis  (IEA,ISO)
visual perception  (IEA)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
COL2A1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11144,196,213 - 44,227,718 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1144,196,094 - 44,227,468 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666037202,151,602 - 202,183,142 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
COL2A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381247,972,967 - 48,006,212 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1247,972,967 - 48,004,554 (-)EnsemblGRCh38hg38GRCh38
GRCh371248,366,750 - 48,398,259 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361246,653,015 - 46,684,552 (-)NCBINCBI36Build 36hg18NCBI36
Build 341246,653,017 - 46,684,528NCBI
Celera1247,164,396 - 47,195,933 (-)NCBICelera
Cytogenetic Map12q13.11NCBI
HuRef1245,398,588 - 45,430,128 (-)NCBIHuRef
CHM1_11248,332,620 - 48,364,163 (-)NCBICHM1_1
T2T-CHM13v2.01247,934,691 - 47,967,944 (-)NCBIT2T-CHM13v2.0
Col2a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391597,873,483 - 97,902,525 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1597,873,483 - 97,902,576 (-)EnsemblGRCm39 Ensembl
GRCm381597,975,602 - 98,004,724 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1597,975,602 - 98,004,695 (-)EnsemblGRCm38mm10GRCm38
MGSCv371597,806,033 - 97,835,155 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361597,803,005 - 97,832,679 (-)NCBIMGSCv36mm8
Celera15100,100,464 - 100,129,552 (-)NCBICelera
Cytogenetic Map15F1NCBI
cM Map1553.97NCBI
Col2a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87130,977,561 - 131,006,627 (-)NCBIGRCr8
mRatBN7.27129,098,489 - 129,127,560 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7129,098,786 - 129,127,546 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx7130,895,443 - 130,924,189 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.07133,120,981 - 133,149,729 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.07133,033,447 - 133,062,197 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.07139,454,945 - 139,484,403 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7139,455,242 - 139,483,997 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07139,646,698 - 139,675,832 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47136,679,219 - 136,707,976 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.17136,755,655 - 136,784,413 (-)NCBI
Celera7125,589,749 - 125,618,504 (-)NCBICelera
RH 3.4 Map71096.2RGD
Cytogenetic Map7q36NCBI
Col2a1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555006,860,771 - 6,885,473 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555006,860,771 - 6,885,466 (-)NCBIChiLan1.0ChiLan1.0
COL2A1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21046,160,541 - 46,192,087 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11246,157,299 - 46,188,845 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01240,726,137 - 40,757,690 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11241,600,206 - 41,631,789 (+)NCBIpanpan1.1PanPan1.1panPan2
COL2A1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1276,756,994 - 6,787,733 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl276,756,994 - 6,787,733 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2739,518,936 - 39,549,645 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0276,824,733 - 6,855,569 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl276,824,865 - 6,855,569 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1276,762,038 - 6,792,716 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0276,796,986 - 6,827,666 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02739,807,429 - 39,838,181 (-)NCBIUU_Cfam_GSD_1.0
Col2a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494567,272,043 - 67,302,897 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365125,861,933 - 5,892,853 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365125,861,933 - 5,894,898 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COL2A1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl578,350,137 - 78,380,718 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1578,350,131 - 78,380,893 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2581,530,406 - 81,554,481 (-)NCBISscrofa10.2Sscrofa10.2susScr3
Col2a1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248164,274,219 - 4,304,513 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248164,273,969 - 4,304,519 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

endocrine system hemolymphoid system nervous system
High
Medium 16 16
Low 4 16 14
Below cutoff 16 4 29

Sequence


Reference Sequences
RefSeq Acc Id: ENSCSAT00000004361   ⟹   ENSCSAP00000002621
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.1 Ensembl1144,196,094 - 44,227,468 (-)Ensembl
RefSeq Acc Id: XM_008003027   ⟹   XP_008001218
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.11144,196,213 - 44,227,718 (-)NCBI
Vero_WHO_p1.0NW_023666037202,151,602 - 202,183,142 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008003028   ⟹   XP_008001219
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.11144,196,213 - 44,227,717 (-)NCBI
Vero_WHO_p1.0NW_023666037202,151,602 - 202,183,142 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_008001218 (Get FASTA)   NCBI Sequence Viewer  
  XP_008001219 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSCSAP00000002621.1
Reference Protein Sequences
RefSeq Acc Id: XP_008001218   ⟸   XM_008003027
- Peptide Label: isoform X1
RefSeq Acc Id: XP_008001219   ⟸   XM_008003028
- Peptide Label: isoform X2
RefSeq Acc Id: ENSCSAP00000002621   ⟸   ENSCSAT00000004361


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCSAG00000006460 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCSAT00000004361.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.120.1000 UniProtKB/TrEMBL
  Complement Module, domain 1 UniProtKB/TrEMBL
InterPro Collagen UniProtKB/TrEMBL
  Fib_collagen_C UniProtKB/TrEMBL
  VWF_dom UniProtKB/TrEMBL
NCBI Gene COL2A1 ENTREZGENE
PANTHER COLLAGEN ALPHA UniProtKB/TrEMBL
  COLLAGEN ALPHA-1(II) CHAIN UniProtKB/TrEMBL
Pfam COLFI UniProtKB/TrEMBL
  Collagen UniProtKB/TrEMBL
  VWC UniProtKB/TrEMBL
PROSITE NC1_FIB UniProtKB/TrEMBL
  VWFC_1 UniProtKB/TrEMBL
  VWFC_2 UniProtKB/TrEMBL
SMART COLFI UniProtKB/TrEMBL
  VWC UniProtKB/TrEMBL
Superfamily-SCOP FnI-like domain UniProtKB/TrEMBL
UniProt A0A0D9R1Y2_CHLSB UniProtKB/TrEMBL